


It Was Raining Then, But The Sun's Setting Now

by SunshineDawn



Category: Marvel Cinematic Universe, Spider-Man (Tom Holland Movies)
Genre: Alternate Universe - Canon Divergence, Angst, Angst with a Happy Ending, Flashbacks, Gen, Identity Reveal, Kid Peter Parker, Other Additional Tags to Be Added, Peter Parker Whump, Peter Parker is a Mess, Peter and MJ are adorable, Sad with a Happy Ending, Time Skips, i dont really know how to tag this, i havent found a fic like this so who knows if people will like this, kinda weird tags
Language: English
Status: In-Progress
Published: 2021-03-09
Updated: 2021-03-09
Packaged: 2021-03-15 15:42:24
Rating: Teen And Up Audiences
Warnings: No Archive Warnings Apply
Chapters: 1
Words: 3,158
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/29935668
Author URL: https://archiveofourown.org/users/SunshineDawn/pseuds/SunshineDawn
Summary: Peter's life through the years. The tragedies, the blessings. Sadly, there's more tragedies then blessings.Peter grows up at Camp Opal, or rather, Orphan Protection Agency. Why he's taken there, he doesn't know. He grows up doing missions, but once he's bitten by the radioactive spider, he becomes a biological weapon for them. Though, once he completes twelve years of training, he's sent on his biggest mission yet. His normality mission. At age 16, he leaves camp to live with May and Ben Parker, for two years. While he's there, he becomes Spiderman, meets Tony, and kicks some ass.Right as he starts making sense of his two mindsets, Soldier Parker and Civilian Parker, he gets kidnapped. Tony has to make some seriously tough calls to get him back, and once he does, will he ever be the same again? Either of them?Because it's raining now, will the sun ever set?
Relationships: Eventual Michelle Jones/Peter Parker - Relationship, Michelle Jones & Peter Parker, Pepper Potts/Tony Stark, Peter Parker & Tony Stark
Kudos: 6





	It Was Raining Then, But The Sun's Setting Now

**Author's Note:**

> Hi!!!! Sunshine Dawn here! 
> 
> I've written a new fic, but this one's a little different. This one has a little bit of childhood trauma, some kidnapping, some identity crises, a guilty tony, and some death.
> 
> I hope you like it, I wanted to write something different. I'll be writing my next chapter of my Percy Jackson fic next. It's a little all over the place, and I hope you can follow it.
> 
> Please be nice, and remember "A kind act can sometimes be as powerful as a sword" -Rick Riordan
> 
> -Sunshine Dawn <3

**_Age 3: July, 2005_ **

May watched as Peter sat on the living room floor, playing with his toys. His Captain America and Howling Commando dolls sprawled across the floor. Ben tucked away in his little corner office in their bedroom, the sun setting through their windows. 

_ Knock, knock, knock _

May got up from her spot on the couch, her slippers scuffing across their carpet, towards her front door. Their apartment was so small that she barely walked ten steps. 

_ Knock, knock, knock _

“Coming!” She yelled.

“Aun’ Ma? Who’s dere?” Peter asked, not looking up from his toys.

“Stay there, okay honey?” May said.

“Otay.” 

May peeked through the peephole. Cops? She backed away from the door, and lowered her voice.

“Peter, baby, can you go tell Uncle Ben I need him? Then stay in your room for me, okay?” 

_ Knock, knock, knock _

Peter copied her tone. “Otay!” He took off running.

A few seconds later, Ben came around the corner. “May? What’s wrong?” 

“I don’t know Ben, it’s the cops.” Ben opened the door part way.

“Hello? How can I help you?” Ben said.

Two cops stood in the hallway. A blonde, Beckett, and a brunette, Wright.

“Sir, may we talk to you and your wife?” Beckett said.

“Can I ask what for?” Ben said, still not opening the door.

“It is about Richard and Mary Parker.” Wright said.

Ben opened the door, May appearing out from behind it.

“What about them?” May asked.

Wright turned to Ben. “Are you the brother of Richard Parker?”

“Yes.” Ben said.

“May we come inside? This information would be better delivered sitting down.” Beckett said.

“Um, sure.” May said, showing the cops inside.

The three sat down at the table, before May went over to Peter’s room.

“Honey, stay in here. I’m gonna close the door, you stay in here playing with your toys. We can watch a movie later okay? We can stay up late if you’re good.” May said.

“Otay. Can we watch Peter Pan?” Peter asked.

“Yea, baby we can. Stay here.” 

“Otay, Aun’ Ma.” Peter went back to playing with his fake tools, as May shut the door and made her way down the hall.

“Okay, now, what’s wrong?” May addressed the cops.

“We are here because you and your husband are willed as next of kin-” Beckett started.

“What? Next of kin?” Ben interrupted.

“And we regret to inform you that Richard Parker and Mary Parker have both passed.” Beckett finished.

“What?” May said. “No, that’s not possible. They’re supposed to be in London on a business trip.” May was frantic. Ben’s face was blank. His eyes empty. “B-Ben, they can’t be..”

“They passed? This isn’t some trick?” His voice was thin, no emotion whatsoever.

“No, sir. They passed around 11am this morning.” Beckett said.

“Can you...do you know how?” Ben asked. May looked at him with wide eyes, her mouth pressed into a line.

“Yes, if you would like to know.” Wright said.

“Please.” May didn’t even know her voice left her throat. 

“A 911 call was made from a crew on a containment ship 200 miles off the coast of new york around seven am about a falling plane. They had said the plane was on fire, and landed in the ocean. We don’t know the cause of why the plane crashed, or how, all we know is by the time the plane was recovered, all passengers were deceased. All seemed to be dead long before the plane even started falling.” 

“Oh my god-” May broke into tears. Ben reached over, and pulled her close, tears and emotions finally coming through.

“Aun’ Ma? Unc’ Ben? Wha’s wrong?” 

“Peter! Peter, go back to your room!” May raised her voice, but her knees were too weak to stand.

“Aun’ Ma?” Peter started to cry.

“Ma’am, may I lead him back to his room?” Wright asked.

“Yes, just-” Her voice lowered to a whisper “don’t- don’t tell him nothing.”

“Yes, ma’am.” Officer Wright got up, and walked over to Peter, who had his Captain America pajamas on by now.

“Hey, kid. You wanna come with me back to your room?” He said, holding out his hand as he kneeled down. 

“But, wha’s wrong with my Aun’ Ma?” 

“She’s just a little sad right now, but my friend Officer Beckett and your Uncle will take care of her okay? Wanna show me your favorite toys?” 

Peter looked reluctant to leave his family. “Um, otay.” He took Wright’s hand and led him to his room.

“Mr. and Mrs. Parker, we have DNA proving their bodies are their bodies, but we need someone to come identify and clarify it is their bodies. If it is alright with you, we’d like to schedule a time for you to come down to the coroner’s office.” Beckett said.

“Um,...yeah. We’ll come identify them.” Ben said.

“Alright. Someone will call you with information.” Beckett pulled out a packet of papers, “This is a packet of info containing information on help pertaining to therapy and mental help. Child aged help and adult.”

“Thank you.” 

“If we may, my officer and I will take our leave now. Someone will be in touch about all the proceeding arrangements.” Beckett said.

“Okay.” Ben said.

Wright came out of Peter’s room. “Thank you, Mr. and Mrs. Parker, and we are truly sorry for your loss.” Beckett and Wright made their way to the door. Ben followed, shutting and locking it behind them. 

“Oh, Ben, what are we gonna do?” May cried quietly, falling into Ben’s arms.

“I don’t know, May. I don’t know.”

“We have to tell Peter. How do we tell him his parents are…” May couldn’t say it.

“He’s smart. He already knows something’s wrong. He’ll be able to see straight through any lies or if we tried to baby him.” Ben said.

“I know. Gosh, I know.” May said.

They didn’t get an answer to their question, because Peter came out of his room.

“Okay?” He asked. 

“Yeah, baby, we’re okay.” May answered.

“But- you’re crying.” May could hear his voice choking up.

“Honey,” May broke away from Ben’s arms and walked over to Peter, picking him up. “We have something to tell you, something big.” 

“A per’prise?” He asked.

“No-” Ben cried, “No. Not a surprise.”

“Let’s go sit down on the couch okay? You can sit in Uncle Ben’s lap, how about that?” She said.

“Otay.” They walked over to the couch, and sat down.

“Peter, you know how mommy and daddy went to work this morning, and they dropped you off before the sun rose?” Ben said.

“Yeah, they left while I sleeped.” Peter responded.

“Well,” May started to cry again. “They didn’t-” May started to sob.

Ben took over again. “Peter, honey, their plane took them to heaven instead of London.” Ben held back tears.

“To heaven?” Peter asked.

“Yeah, baby. They went up to meet the angels.” May said.

Peter sat in silence for a while. May and Ben said nothing as they watched Peter’s thoughts race behind his little eyes, trying to wrap his mind around it.

“When will mommy and daddy get home?”

“Petey,” Ben stopped. “Mommy and daddy’s new job is to keep the angels healthy. Like they did you.”

“But mommy and daddy always come back.” Peter started to panic.

“They have to work with the angels now. They- they are going to live with them now.” May said.

“But, mommy pro’ised. Mommy said she come back!” Peter threw himself off Ben’s lap onto the floor. He was crying.

“Her and daddy can’t come back, baby. They can’t.” May crawled on the floor with Peter, pulling him to her.

“No!” Peter screamed. He pushed against May.

“Peter Pan, can you calm down? Please breathe for me, Pete.” Ben said, sitting down on the floor next to them.

Peter struggled to breathe. “I want mommy! I want daddy!” 

“I know, baby. I want them too.” Ben said. He held May and Peter tight, as they cried together on the floor.

It was raining now.

  
  


**_Twelve Years Later, Age 16: August, 2017_ **

_ Thwip Thwip _

“That’s good Parker! Let’s see how you handle against some lasered drones!”

“Yes sir!” Peter yelled from sixty feet above.

Three black drones shooting lasers flew at high speeds to Peter, with one movement, he released his web attached to the ceiling, kicked and shattered two drones, shot another and landed on the third, smashing through it’s core with his fist.

“Good! Not a scratch this time! Let’s take ten!” 

“Yes, sir!” Peter yelled, webbing to a wall and jumping down.

Peter lived, trained and served at a Camp called Opal, Orphan Protection Agency Level: Four. The levels were just signifying that the children at levels one through three were just normal children. Level four, however, they trained day and night to become soldiers, spies, agents. They all trained for different purposes. Some trained especially in science, others in combat. Peter walked over the blue mats and out of the steel walled gym. He trained in everything. For combat however, this gym had been specialty built for him two years ago, when he came back from that fatal mission.

**_Two Years Before Age 14: 2015_ **

“Get him on the bed! Turn him on his side!” 

Peter seized as two men carried him into the medical facility, nurses and doctors scrambling to find out what was wrong with their best agent. 

“Ma’am his mouth is foaming!” One of the men holding him panicked.

“10 milligrams of Diazepam! Shoot this into his leg!” The main nurse yelled. The man grabbed the syringe, and stabbed it into Peter’s leg. Peter didn’t stop seizing.

“He didn’t calm!” 

“We have to up the dose!” The nurse yelled. “Another 10 milligrams!” The nurse shot this one into his leg, and Peter finally stilled.

“I want to figure out what’s wrong with him as quickly as we can! Get his partner here! I need to know what happened!” The doctor said.

The two men ran out, followed by the doctor. The nurses could handle him for now.

“General, I have to know what happened to Peter if I am going to treat him. He won’t stop seizing, his fever is 112, and no drugs are working!” The doctor said, his hands moving frantically with each word.

“His partner was the same as always; Michelle Jones. She hasn’t given her report yet but we can skip the protocol for now, follow me.” The general said.

The general and the doctor took off to retrieve Michelle from her own physical. 

“Agent Jones! What happened to Peter?” The general ordered.

“I am not sure, sir. We got separated by security, and by the time I caught up I found his two security guards unconscious, and down the hall an open door labeled restricted. He was unconscious on the floor. We were surrounded by glass tanks full of animals, and signs saying radioactive. He had a bite mark on his wrist.” She said with no emotion in her voice.

“Do you know what bit him?” The doctor asked.

“No, sir, though my guess is it was a spider, as there was a dead spider on the floor next to him. I called for backup after that.”

“A radioactive spider, which we have no clue what it was altered with. Just great.” The doctor exclaimed as he turned and ran back to Peter’s separate room. 

“He was bit by a radioactive spider.” He yelled to the nurses, but as he turned the corner into the room, the nurses were all standing helplessly by as Peter laid still, completely still.

“Sir, he isn’t breathing but his heart rate and oxygen levels are still going. His fever is only getting higher.” A nurse said.

“Can you fix him?” The general asked from the doorway.

“Not if I don’t know why he’s sick.” The doctor said.

**_Age 16: August, 2017_ **

  
  


Peter flung open the metal doors, a smile on his face. Training had gone well. He passed offices and classrooms, labs and storage. Signs labeled his way to the mess hall, where he was meeting up with his best friend and mission partner, Michelle Jones.

Peter walked through the lunch line, the lunch ladies piling food onto his plate. He then stopped at the end, slid his card to prove he ate that meal, and was given two extra protein bars, which were specially designed for him. Peter needed four times as many calories as the normal soldier his age needed, because he was known as a bio-weapon, or even a super soldier. Finally, he made it to the table where MJ sat alone.

“Hey, guys.” Peter said.

“Hey Peter Pan, how are you?” MJ said. Peter Pan. That was MJ’s special nickname for him. They were the same age, and had both been sent to Camp Opal twelve years ago when their parents passed. 

“I made it through 37 drones today with no injuries. I may just be able to go on my normality mission soon!” Peter said, his grin practically splitting apart his face.

“I have no clue why your excited about some stupid mission. Let alone the normality mission. We have to live for two years as normal citizens, doing normal high school shit. We’re grades ahead our age, and we could kill someone in sixty three different ways using just our bodies. I find it useless.” MJ said.

“It’ll be fun, MJ. We get to see what it’s like for kids who didn’t grow up in a secret clandestine base training to work for the government.” 

“No. No it will not. I am not excited to live with a bunch of snot nosed people who think that their life matters. In the grand scheme of things, no one’s life matters. People are so conceited to think that their measly little 70 years on this planet is going to mean anything in the billion of years we’ve floated in the dark vacuum of space.” 

“Well that’s dark.” Peter said.

“Life’s dark.” MJ said. They both busted out laughing.

“Well, I’m excited because I already got my assignment.” 

“What? They gave you it already?” MJ looked shocked, and if not a little jealous.

“Do I detect jealousy, Miss Jones?” Peter teased.

“Peter Parker if you do not tell me when the fuck you are leaving I will dismember you.” MJ threatened.

“Okay, okay calm down, MJ.” Peter said.

“Speak.”

“I’m going to live with my own family. My aunt and uncle, who both live in Queens, New York. I leave September 10th.” Peter said.

“What? You still have family on the outside? Why are you here?” MJ had lost her playful mood.

“Apparently my parents had it in their will that should they die, I would come here. Specifically, this camp.” 

“So, you’ve met these people before? The ones you’re going to live with?” MJ asked.

“I guess. I mean, I came here at four so I can imagine I’ve met them before. Not that I remember it. Their names are Ben and May Parker. Ben is my father’s brother.” Peter said.

“Wow. And you leave so soon. That’s in two weeks.” 

“I guess they were able to meet all requirements early. Usually it takes months.” Peter said.

“Do you know anything else?” MJ asked.

“Not really. Just that I’ll be homeschooled for the first few months and then I might go to regular school. Just because of my enhanced senses, they don’t know if a large city like New York would overstimulate my senses.” 

“I can’t believe it. You’ve completed the twelve years of training. I’ve completed the twelve years of training. Soon we can be real operatives.” MJ said.

“I’m not too excited for that part.” Peter said. His voice quieted.

“Wait, why?” MJ’s voice lowered too.

“Grown operatives kill.” He said.

“And we don’t cause we’re still underaged.” MJ finished. 

“Yeah. And I know how to kill, but I don’t think I could. Take someone’s life? I feel like I’d be taking mine everytime.” Peter said.

“Well, how about this. We sign up as partners. That way, our missions are always together. I’ll do the killing since they’re bad guys, and you do all our paperwork.”

“Deal.” Peter smiled.

**_Age 16: September 10, 2017_ **

A plane’s blades cut through the air, creating a loud sound that hurt Peter’s ears slightly.

MJ walked towards Peter. She’d been given early release to say goodbye to Peter, which took a lot of begging from them both to their officers.

“I can’t believe it. This is our first mission apart. Who’s gonna keep you alive after you get bitten by a radioactive spider?” MJ joked.

“I’ll be okay on my own, MJ. Don’t fatally wound anyone at your new home, that would be bad.” Peter laughed.

“Even if they deserve it?”

“Even if they deserve it.”

“Agent Parker, we have wheels up in ten.” An older agent yelled.

“I’ll see you in two years, okay? Don’t do anything stupid.” Peter said.

“You’re taking all the stupid with you. I’ll be fine.” MJ laughed. To most, MJ looked bored right now. Peter, well he knew she was on the edge of tears.

“I love you okay? Best friends forever.” Peter said.

“Best friends. I’ll miss you, okay? Don’t make any new best friends, cause I couldn’t live without you.” Peter was a little shocked. MJ never showed or even said her emotions like this.

“I will never. When you get your assignment, send me a letter. You have the address of mine, right?” 

“Yeah, I do.”

“Good.” Peter reached in to hug MJ.

Arms wrapped tight around each other, Peter let a few tears fall. “Make sure you are actually here when I get back okay? I can’t be visiting you in two years if you’re six feet under.” 

“Same goes for you.” MJ slipped a book into Peter’s small bag he was holding. “Don’t look at that till you get to your new place, okay? If the others see it, they’ll take it.” 

Peter remembered one of the biggest rules. No taking anything out of base that wasn’t assigned by the officers. “Okay. I left something under your pillow. Got it on the last mission, while you were infiltrating that building.” 

MJ pulled away so she could look at Peter and his teary face. “Oh you mean the mission where I almost got killed because you forgot to man comms? That mission?”

“Yeah, that mission.”

MJ pulled Peter tight again. “I love you, Peter Pan. Stay safe.”

“I love you too.” Peter let go of MJ. He let go of the life he knew till now.

Peter walked up the stairs to the small plane, and gazed out the window back at MJ crying softly on the ground. As he flew away from the life he’d lived for the last 12 years, his eyes only saw MJ.


End file.
